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<div class=Section1>

<h1><a name="_Toc111992856"></a><a name="_Toc112582956"></a><a
name="_Princeton_multi-voxel_pattern"></a><span style='mso-bookmark:_Toc111992856'><span
style='mso-bookmark:_Toc112582956'>Princeton multi-voxel pattern analysis </span></span>&#8211;
discarded</h1>

<p class=MsoNormal align=right style='margin-top:2.0pt;mso-margin-bottom-alt:
auto;text-align:right'>16/08/2005</p>

<p class=MsoNormal align=right style='margin-top:2.0pt;mso-margin-bottom-alt:
auto;text-align:right'>Version 1</p>

<p class=MsoNormal><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<h2><a name="_Toc111992859"></a><a name="_Toc112582921"></a><a
name="_Toc112582966"><span style='mso-bookmark:_Toc112582921'><span
style='mso-bookmark:_Toc111992859'><span lang=EN-US style='mso-ansi-language:
EN-US'>Why do classification at all?<u1:p></u1:p></span></span></span></a><span
lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></h2>

<p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'>In answer,
we point you towards:<o:p></o:p></span></p>

<p class=MsoNormal style='margin-top:4.0pt;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt'><span lang=EN-US style='color:red;
mso-ansi-language:EN-US'>Haxby et al. (Science, 2001)</span><span lang=EN-US
style='color:blue;mso-ansi-language:EN-US'><o:p></o:p></span></p>

<p class=MsoNormal style='margin-top:4.0pt;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt'><span lang=EN-US style='color:red;
mso-ansi-language:EN-US'>Mitchell et al.</span><span lang=EN-US
style='color:blue;mso-ansi-language:EN-US'><o:p></o:p></span></p>

<p class=MsoNormal style='margin-top:4.0pt;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt'><span lang=EN-US style='color:red;
mso-ansi-language:EN-US'>Polyn thesis</span></p>

<h2>Excluding TRs</h2>

<p class=MsoNormal>This is the procedure:</p>

<ul style='margin-top:0cm' type=disc>
 <li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list 36.0pt'>Create
     a new regressors object by duplicating the current set of regressors. Then
     remove the appropriate condition-rows from the new regressors. That should
     leave lots more 'rest timepoints', i.e. timepoints with no active
     conditions.</li>
</ul>

<p class=MsoNormal>Don't delete any TRs from your patterns or regressors.</p>

<p class=MsoNormal>Then, create a new selectors object that consists of 1s.
Label TRs from the conditions that you want to exclude with zeros. Now, when
you call <i>create_xvalid_indices.m</i>, feed in this extra selectors object as
the <i>actives_selname</i>, and the analyses from this point onwards that
depend on the xvalid indices (e.g. the no-peeking statmap creation and
cross-validation classification) will exclude those zero-TRs.</p>

<p class=MsoNormal>The main advantage of this method is that it doesn't require
you to actually delete the TRs that you don't want from your patterns, so that
if you change your mind, you can easily rerun your analysis by feeding in a
different actives_selname selector to <i>create_xvalid_indices.m</i>.</p>

<p>Here's an example. Imagine we have 3 conditions to begin with, stored in the
<i>regs_original</i> regressors object. The conditions themselves are called
'condA', 'condB' and 'condC', and we want to create a new regressors object
called <i>regs_no_c </i>that excludes 'condC'. We should also make sure to update
the condnames field, to reflect which conditions are now stored in the <i>regs_no_c</i>
object.</p>

<div style='border:solid windowtext .25pt;padding:6.0pt 3.0pt 6.0pt 3.0pt'>

<p class=Code>&gt;&gt; subj = duplicate_object(subj,'regressors','regs_original','regs_no_c);</p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; regs_nocondc = get_mat(subj,'regressors',regs_no_c');</p>

<p class=Code>&gt;&gt; regs_no_c(3,:) = [];</p>

<p class=Code>&gt;&gt; subj = set_mat(subj,'regressors',regs_no_c);<o:p></o:p></p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; condnames_no_c = get_objfield(subj,'regressors','regs_no_c',condnames);</p>

<p class=Code>&gt;&gt; condnames_no_c(3) = [];</p>

<p class=Code>&gt;&gt; subj = set_objfield(subj,'regressors','regs_no_c','condnames',condnames_no_c);</p>

</div>

<p>Now, create a selector (with the same number of timepoints as the regressors
matrix), which we'll call <i>sel_no_condc</i>. TRs from conditions we want will
have a 1 &#8211; all others will be zeros.</p>

<div style='border:solid windowtext .25pt;padding:6.0pt 3.0pt 6.0pt 3.0pt'>

<p class=Code>&gt;&gt; sel_no_c = ones(1,size(conds_no_c,2)); </p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; TRs_to_keep = any(sum(regs_no_c));</p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; subj = init_object(subj,'selector','sel_no_c');<o:p></o:p></p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; subj = set_mat(subj,'selector','sel_no_c',sel_no_c');</p>

</div>

<p>Finally, call <i>create_xvalid_indices.m</i>, feeding in the <i>sel_nocondc</i>
as the optional <i>actives_selname</i> selector.</p>

<div style='border:solid windowtext .25pt;padding:6.0pt 3.0pt 6.0pt 3.0pt'>

<p class=Code>&gt;&gt; subj = create_xvalid_indices(subj,'runs', ...</p>

<p class=Code><span style="mso-spacerun:
yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
style="mso-spacerun:
yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
style="mso-spacerun: yes">&nbsp;</span>'actives_selname','sel_no_c');</p>

</div>

<p class=MsoNormal>Note: our current recommendation is to include all the
timepoints in your data when zscoring, including conditions that you don't want
and rest data. As a result, there is no functionality included in <i>zscore_runs.m</i>
for excluding timepoints.</p>

<p class=MsoNormal><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p>Now, create a selector (with the same number of timepoints as the regressors
matrix), which we'll call <i>sel_no_condc</i>. TRs from conditions we want will
have a 1 &#8211; all others will be zeros.</p>

<div style='border:solid windowtext .25pt;padding:6.0pt 3.0pt 6.0pt 3.0pt'>

<p class=Code>&gt;&gt; sel_no_c = ones(1,size(conds_no_c,2)); </p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; TRs_to_keep = any(sum(regs_no_c));</p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; subj = init_object(subj,'selector','sel_no_c');<o:p></o:p></p>

<p class=Code><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

<p class=Code>&gt;&gt; subj = set_mat(subj,'selector','sel_no_c',sel_no_c');</p>

</div>

<p>Finally, call <i>create_xvalid_indices.m</i>, feeding in the <i>sel_nocondc</i>
as the optional <i>actives_selname</i> selector.</p>

<div style='border:solid windowtext .25pt;padding:6.0pt 3.0pt 6.0pt 3.0pt'>

<p class=Code>&gt;&gt; subj = create_xvalid_indices(subj,'runs', ...</p>

<p class=Code><span style="mso-spacerun:
yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
style="mso-spacerun:
yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
style="mso-spacerun: yes">&nbsp;</span>'actives_selname','sel_no_c');</p>

</div>

<p class=MsoNormal>Note: our current recommendation is to include all the
timepoints in your data when zscoring, including conditions that you don't want
and rest data. As a result, there is no functionality included in <i>zscore_runs.m</i>
for excluding timepoints.</p>

<p class=MsoNormal><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>

</div>

<u1:p></u1:p><u1:p></u1:p>
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